Steve Blair

Resonant-enhanced evanescent-wave fluorescence biosensing with cylindrical optical cavities

We show that the artificial resonances of dielectric optical cavities can be used to enhance the detection sensitivity of evanescent-wave optical fluorescence biosensors to the binding of a labeled analyte with a biospecific monolayer. Resonant coupling of power into the optical cavity allows for efficient use of the long photon lifetimes (or equivalently, the high internal power) of the high-Q whispering gallery modes to increase the probability of photon absorption into the fluorophore, thereby enhancing fluorescence emission. A method to compare the intrinsic sensitivity between resonant cavity and waveguide formats is also developed. Using realistic estimates for dielectric cylindrical cavities in both bulk and integrated configurations, we can expect sensitivity enhancement by at least an order of magnitude over standard waveguide evanescent sensors of equivalent sensing geometries. In addition, the required sample volume can be reduced significantly. The cylindrical cavity format is compatible with a large variety of sensing modalities such as immunoassay and molecular diagnostic assay.

Fluorescence enhancement from an array of subwavelength metal apertures.

We report the resonant excitation of a fluorescing molecular monolayer applied to a periodic array of subwavelength apertures in a metal film. The peak fluorescence occurs under conditions of maximum transmission of the excitation light, which indicates strong enhancement of the incident light within the apertures under resonant conditions. Fluorescence output normalized to the aperture fill fraction is enhanced by nearly 40 times, and the rate of photobleaching is increased by approximately a factor of 2, suggesting an increase in the fluorescence yield.

Second-harmonic generation from an array of sub-wavelength metal apertures

We demonstrate the generation of second-harmonic radiation in transmission through periodic and disordered arrays of sub-wavelength metallic apertures. For circular apertures in a square lattice, the second-harmonic signal peaks at incidence angles corresponding to enhanced transmission of the fundamental beam of 800 nm wavelength except at small incidence angles where the local symmetry minimizes the effective second-order nonlinear susceptibility of the apertures. Even though the linear transmission of the fundamental beam can be more than five times greater through the periodic array as compared to a disordered array, the strength of the second harmonic from the disordered array is greater at large incidence angles. By breaking the local symmetry through the use of apertures of non-centrosymmetric shape, the second-harmonic output occurs at fundamental transmission resonances at small incidence angles.

Biosensing based upon molecular confinement in metallic nanocavity arrays

We describe the basis for an affinity biosensor platform in which enhanced fluorescence transduction occurs through the optical excitation of molecules located within metallic nanocavities. These nanocavities are about 200 nm in diameter, are arranged in periodic or random two-dimensional arrays, and are fabricated in 70 nm thick gold films by e-beam lithography using negative e-beam resist. The experimental results show that both periodic and randomly placed metallic nanocavities can be used to enhance the fluorescence output of molecules within the cavities by about a factor of ten. In addition, the platform provides isolation from fluorescence produced by unbound species, making it suitable for real-time detection. Finally, we demonstrate the use of the platform in the real-time detection of 20-base oligonucleotides in solution.

Direct DNA Methylation Profiling Using Methyl Binding Domain Proteins

Methylation of DNA is responsible for gene silencing by establishing heterochromatin structure that represses transcription, and studies have shown that cytosine methylation of CpG islands in promoter regions acts as a precursor to early cancer development. The naturally occurring methyl binding domain (MBD) proteins from mammals are known to bind to the methylated CpG dinucleotide (mCpG) and subsequently recruit other chromatin-modifying proteins to suppress transcription. Conventional methods of detection for methylated DNA involve bisulfite treatment or immunoprecipitation prior to performing an assay. We focus on proof-of-concept studies for a direct microarray-based assay using surface-bound methylated probes. The recombinant protein 1xMBD-GFP recognizes hemimethylation and symmetric methylation of the CpG sequence of hybridized dsDNA, while displaying greater affinity for the symmetric methylation motif, as evaluated by SPR. From these studies, for symmetric mCpG, the K(D) for 1xMBD-GFP ranged from 106 to 870 nM, depending upon the proximity of the methylation site to the sensor surface. The K(D) values for nonsymmetrical methylation motifs were consistently greater (>2 muM), but the binding selectivity between symmetric and hemimethylation motifs ranged from 4 to 30, with reduced selectivity for sites close to the surface or multiple sites in proximity, which we attribute to steric effects. Fitting skew normal probability density functions to our data, we estimate an accuracy of 97.5% for our method in identifying methylated CpG loci, which can be improved through optimization of probe design and surface density.

Second-harmonic emission from sub-wavelength apertures: Effects of aperture symmetry and lattice arrangement

We measure second-harmonic generation from arrays of sub-wavelength apertures in transmission using fundamental input at 800 nm. Lattice arrangements include disordered, Penrose (quasi-periodic or aperiodic), and square (periodic). Strong angular dependence of SHG is observed, with maxima located at angular positions that roughly correspond to incidence angles of extraordinary optical transmission (EOT) for the fundamental. In addition, even at incidence normal to the sample, strong secondary maxima are observed at off-normal scattering angles for the arrangements with higher degree of order. Breaking the inversion symmetry of the aperture allows second harmonic peaks at normal incidence and detection. These measurements help to resolve the role that symmetry plays in second-harmonic generation from arrays of apertures.

A 3D glass optrode array for optical neural stimulation

This paper presents optical characterization of a first-generation SiO2 optrode array as a set of penetrating waveguides for both optogenetic and infrared (IR) neural stimulation. Fused silica and quartz discs of 3-mm thickness and 50-mm diameter were micromachined to yield 10 × 10 arrays of up to 2-mm long optrodes at a 400-μm pitch; array size, length and spacing may be varied along with the width and tip angle. Light delivery and loss mechanisms through these glass optrodes were characterized. Light in-coupling techniques include using optical fibers and collimated beams. Losses involve Fresnel reflection, coupling, scattering and total internal reflection in the tips. Transmission efficiency was constant in the visible and near-IR range, with the highest value measured as 71% using a 50-μm multi-mode in-coupling fiber butt-coupled to the backplane of the device. Transmittance and output beam profiles of optrodes with different geometries was investigated. Length and tip angle do not affect the amount of output power, but optrode width and tip angle influence the beam size and divergence independently. Finally, array insertion in tissue was performed to demonstrate its robustness for optical access in deep tissue.

Third-harmonic generation from arrays of sub-wavelength metal apertures

We measure third-harmonic generation (THG) from arrays of sub-wavelength metal apertures in transmission using fundamental input at 800 nm. Samples with different aperture spacings, sizes, and shapes are used. Strong angular dependence of THG is observed, with maxima located at incidence angles corresponding to extraordinary optical transmission (EOT) for the fundamental. We demonstrate an anomalous scaling of TH intensity with aperture size, where at different EOT peaks, the TH may either increase or decrease with aperture size. The aperture shape is also shown to have a strong effect on TH output.

Nonlinear phase shift of cascaded microring resonators

We study cascaded microring resonator (CMRR) configurations as general nonlinear phase-shifting elements that exhibit enhanced nonlinear sensitivity and flattened transmission characteristics. We show that even when the material itself has large two-photon absorption, CMRR devices with five rings facilitate a factor-of-10 enhancement of the optical nonlinearity when compared with a channel waveguide having the same group delay. In addition, high throughput in intensity can be maintained up to a 3π phase shift.

Beyond the absorption-limited nonlinear phase shift with microring resonators

We show that the nonlinear phase shift produced by a ring resonator constructed from a given nonlinear optical material can be greater than the phase shift produced by a single pass through an infinite length of the same material when linear and nonlinear absorption are taken into consideration. The figure of merit (defined by the phase shift times the throughput) also improves for the ring resonator over that of the native nonlinear absorbing material. We finally show that these benefits of using the ring resonator as a nonlinear phase-shifting element can enhance the switching characteristics of a Mach-Zehnder interferometer.